A Novel Intragenic Marker Targeting The Ectodomain Of Bacterial Blight-Resistance Gene Xa21 For Marker-Assisted Selection In Rice

The rice (Oryza sativaL.)Xa21gene is known to confer resistance againstXanthomonas oryzaepv.oryzae, the causal organism of bacterial blight (BB) through its involvement in pathogen recognition and immunity responses. The closely linked sequence-tagged site markerpTA248is frequently used for marker-assisted selection (MAS) ofXa21. However, lower precision and linkage drag of linked-markers hinders its reliability and effectiveness in MAS compared to flanking/intergenic markers. In the current study, a diagnostic intragenic marker was developed for MAS ofXa21in rice. The new markerABUOP0001targets a 19-bp insertion/deletion on the ectodomain ofXa21and amplifies a 200-bp amplicon from rice line IRBB 62 (known to carry the "resistance allele"), and a 181-bp amplicon from IRBB 7 (known to carry the "susceptible allele"). TheABUOP0001marker assay identified the resistance allele in 15 rice lines/accessions. In a field study, 14 of these lines/accessions had highly resistant BB responses, and one had an intermediate response. Further,Xa21resistance allele was identified in 1,675 rice accessions through anin-silicogenomic sequence analysis. The markerABUOP0001performs better than the previously used linked-markerpTA248(anchored to a gene 225 kbp upstream ofXa21) asABUOP0001is an intragenic marker targeting the functionally important ectodomain ofXa21. Further,ABUOP0001is compatible for high-throughput screening with high-resolution melting and can be multiplexed effectively with an intragenic marker of BB resistance geneXa4. Therefore,ABUOP0001can be recommended as a high-throughput diagnostic intragenic marker for MAS of Xa21 in rice.